Dr. Alexander Donath

Head of Section
Head of HPC units

Computational Genomics, High-performance Computing

Tel: +49 228 9122-344

Fax: +49 228 9122-295

Mail: a.donath [at] leibniz-zfmk.de

Tabs

Profile

Research interests

Mitochondrial genome evolution
Analysis of transcriptomes and genomes to answer phylogenetic questions
Rare genomic changes

Further information

Software: gappy v1.0

gappy extracts splids (split-inducing indels) from a given alignment and creates a binary absence/presence matrix. gappy is implemented in the C++.

The tool reads multiple sequence alignments in FASTA format. The user can select a minimum and maximum indel length for determining splids. By default, the output is a FASTA file, containing the binary coded splid absence/presence information, and some summary statistics.

Output is also available in PHYLIP and NEXUS format.

Projects

2022

DeRGA - Deutscher ReferenzGenom Atlas

German hub of the European Reference Genome AtlasBuilding up to the mission of the international ERGA, the German biodiversity genomics community aims at generating high-quality reference genomes of the German eukaryotic biodiversity:

Unit:

Comparative Vertebrate Genomics, Computational Genomics, High-performance Computing, Comparative Insect Genomics, Lepidoptera

Project lead:

Astrid Böhne

2017

Evolution of Dexiarchia

The sea slugs of the subgroup Dexiarchia comprise at least 2,000 different species and many more undescribed members. Until today there exists no phylogenetic analysis of Dexiarchia that comprises all major families and corroborates the relationships within this group, which is the aim of our project.

Unit:

Computational Genomics, High-performance Computing, Phylogenetics and Evolutionary Biology, Morphology Laboratory, Chair Molecular Biodiversity Research

Project lead:

Dr. Alexander Donath

Funding:

Deutsche Forschungsgemeinschaft

2014

Immunobiology of the marine…

Investigation of the innate immune system of the heterobranch genus Aplysia.

Unit:

Computational Genomics

Project lead:

Dr. Alexander Donath

Funding:

Zoological Research Museum Alexander Koenig

2012

Leaf beetles - Chrysomelidae

Transcriptome analysis of leaf beetles.

Unit:

Computational Genomics

Project lead:

Dr. Alexander Donath

Funding:

University of Hamburg

1KITE: The evolution of the insects

Insects are one of the most species-rich groups of metazoan organisms. They play a pivotal role in most non-marine ecosystems and many insect species are of enormous economical and medical importance. Unraveling the evolution of insects is essential for understanding how life in terrestrial and limnic environments evolved. The 1KITE (1K Insect Transcriptome Evolution) project aims to study the transcriptomes (that is the entirety of expressed genes) of 1,000 insect species encompassing all recognized insect orders. For each species, so-called ESTs (Expressed Sequence Tags) will be produced…

Unit:

Directorate, Chair Systematic Zoology, Directorate Staff, Biodiversity Informatics, Computational Genomics, High-performance Computing, Statistical Phylogenetics and Phylogenomics, Staff Council, Centre for Biodiversity Monitoring and Conservation Science (zbm), Education, Biobank, Hymenoptera, Chair Molecular Biodiversity Research, Centre for Molecular Biodiversity Research (zmb)

Project lead:

Prof. Dr. Bernhard Misof

2009

MITOS

A metazoan mitochondrial genome annotation server.

Unit:

Computational Genomics

Project lead:

Dr. Alexander Donath

Funding:

Deutsche Forschungsgemeinschaft, German Academic Exchange Service, University of Strasbourg, ANR MITOMOT, Alexander von Humboldt-Foundation

External projects

"Metazoan Mitochondrial Genome Annotation"

About 2000 completely sequenced mitochondrial genomes, together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs, are available from the NCBI RefSeq database. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations, in particular for the RNA genes. This causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes.

MITOS (MITOchondrial genome annotation Server) is an automated pipeline that tackles the problem of reliable metazoan mitochondrial genome annotation, using state of the art methods. Protein coding genes are annotated by means of a sophisticated aggregation procedure based on BLAST searches, which allows for the detection of frameshifts, duplication events, and split genes. Structural conservation is utilized for non-coding RNA annotation by employing novel covariance models.

MITOS allows for a systematic error screening, the standardization of gene name and gene boundary designation, anticodon labeling of tRNAs, and provides the means for the assessment of the validity of a gene assignment. The results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time biases, inconsistencies of nomenclature, and typos originating from manual curation strategies are avoided.

The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.

Publications

Published in

2018

Johnson, K.P., Dietrich, C.H., Friedrich, F., Beutel, R.G., Wipfler, B., Peters, R.S., Allen, J.M., Petersen, M., Donath, A., Walden, K.K.O., Kozlov, A.M., Podsiadlowski, L., Mayer, C., Meusemann, K., Vasilikopoulos, A., Waterhouse, R.M., Cameron, S.L., Weirauch, C., Swanson, D.R., Percy, D.M., Hardy, N.B., Terry, I., Liu, S., Zhou, X., Misof, B., Robertson, H.M., Yoshizawa, K., (2018): Phylogenomics and the evolution of hemipteroid insects. Proceedings of the National Academy of Sciences: 201815820.

[more]

Melo Clavijo, J., Donath, A., Serôdio, J., Christa, G. (2018): Polymorphic adaptations in metazoa to establish and maintain photosymbioses. Biological Reviews, 93(4): 2006-2020

[more]

2017

Li, Y., Zhang, R., Liu, S., Donath, A., Peters, R.S., Ware, J., Misof, B., Niehuis, O., Pfrender, M.E., Zhou, X. (2017): The molecular evolutionary dynamics of oxidative phosphorylation (OXPHOS) genes in Hymenoptera. BMC Evolutionary Biology. 17(1), 269. https://doi.org/10.1186/s12862-017-1111-z

[more]

Bank, S., Sann, M., Mayer, C., Meusemann, K., Donath, A., Podsiadlowski, L., Kozlov, A., Petersen, M., Krogmann, L., Meier, R., Rosa, P., Schmitt, T., Wurdack, M., Liu, S., Zhou, X., Misof, B., Peters, R.S., Niehuis, O., (2017): Transcriptome and target DNA enrichment sequence data provide new insights into the phylogeny of vespid wasps (Hymenoptera: Aculeata: Vespidae). Molecular Phylogenetics and Evolution 116, 213–226. https://doi.org/10.1016/j.ympev.2017.08.020

[more]

Petersen, M., Meusemann, K., Donath, A., Dowling, D., Liu, S., Peters, R.S., Podsiadlowski, L., Vasilikopoulos, A., Zhou, X., Misof, B., Niehuis, O. (2017): Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes. BMC Bioinformatics. 18(1), 111. https://doi.org/10.1186/s12859-017-1529-8

[more]

Dowling, D., Pauli, T., Donath, A., Meusemann, K., Podsiadlowski, L., Petersen, M., Peters, R.S., Mayer, C., Liu, S., Zhou, X., Misof, B., Niehuis, O. (2017): Phylogenetic Origin and Diversification of RNAi Pathway Genes in Insects. Genome Biology and Evolution 8(12), 3784-3793. doi:10.1093/gbe/evw281

[more]

GREVE C, RUIZ-TAGLE LM, SIVALINGAM S, LUDWIG KU, WÄGELE H, DONATH A. (2017) The complete mitochondrial genome of the ‘solar-powered’ sea slug Plakobranchus cf. ocellatus (Heterobranchia: Panpulmonata: Sacoglossa) Mitochondrial DNA Part B: Resources, 2(1): 130-131

[more]

Peters, R.S., Krogmann, L., Mayer, C., Donath, A., Gunkel, S., Meusemann, K., Kozlov, A., Podsiadlowski, L., Petersen, M., Lanfear, R., Diez, P.A., Heraty, J., Kjer, K.M., Klopfstein, S., Meier, R., Polidori, C., Schmitt, T., Liu, S., Zhou, X., Wappler, T., Rust, J., Misof, B., Niehuis, O. (2017): Evolutionary History of the Hymenoptera. Current Biology. 27, 1013–1018. https://doi.org/10.1016/j.cub.2017.01.027

[more]

2016

Pauli, T., Vedder, L., Dowling, D., Petersen, M., Meusemann, K., Donath, A., Peters, R.S., Podsiadlowski, L., Mayer, C., Liu, S., Zhou, X., Heger, P., Wiehe, T., Hering, L., Mayer, G., Misof, B., Niehuis, O. (2016): Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects. BMC Genomics 17, 861. doi:10.1186/s12864-016-3205-1

[more]

Mayer, C., Sann, M., Donath, A., Meixner, M., Podsiadlowski, L., Peters, R.S., Petersen, M., Meusemann, K., Liere, K., Wägele, J.-W., Misof, B., Bleidorn, C., Ohl, M., Niehuis, O. (2016): BaitFisher: A software package for multispecies target DNA enrichment probe design. Molecular Biology and Evolution doi:10.1093/molbev/msw056

[more]

2015

Kjer KM, Ware JL, Rust J, Wappler T, Lanfear R, Jermiin LS, Zhou X, Aspöck H, Aspöck U, Beutel RG, Blanke A, Donath A, Flouri T, Frandsen PB, Kapli P, Kawahara AY, Letsch H, Mayer C, McKenna DD, Meusemann K, Niehuis O, Peters RS, Wiegmann BM, Yeates DK, von Reumont BM, Stamatakis A, Misof B. (2015): INSECT PHYLOGENOMICS. Response to Comment on "Phylogenomics resolves the timing and pattern of insect evolution". – Science 349: 487.

[more]

2014

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomáš Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas R. Buckley, Brett Calcott, Junqing Chen, Frank Friedrich, Makiko Fukui, Mari Fujita, Carola Greve, Peter Grobe, Shengchang Gu, Ying Huang, Lars S. Jermiin, Akito Y. Kawahara, Lars Krogmann, Martin Kubiak, Robert Lanfear, Harald Letsch, Yiyuan Li, Zhenyu Li, Jiguang Li, Haorong Lu, Ryuichiro Machida, Yuta Mashimo, Pashalia Kapli, Duane D. McKenna, Guanliang Meng, Yasutaka Nakagaki, José Luis Navarrete-Heredia, Michael Ott, Yanxiang Ou, Günther Pass, Lars Podsiadlowski, Hans Pohl, Björn M. von Reumont, Kai Schütte, Kaoru Sekiya, Shota Shimizu, Adam Slipinski, Alexandros Stamatakis, Wenhui Song, Xu Su, Nikolaus U. Szucsich, Meihua Tan, Xuemei Tan, Min Tang, Jingbo Tang, Gerald Timelthaler, Shigekazu Tomizuka, Michelle Trautwein, Xiaoli Tong, Toshiki Uchifune, Manfred G. Walzl, Brian M. Wiegmann, Jeanne Wilbrandt, Benjamin Wipfler, Thomas K. F. Wong, Qiong Wu, Gengxiong Wu, Yinlong Xie, Shenzhou Yang, Qing Yang, David K. Yeates, Kazunori Yoshizawa, Qing Zhang, Rui Zhang, Wenwei Zhang, Yunhui Zhang, Jing Zhao, Chengran Zhou, Lili Zhou, Tanja Ziesmann, Shijie Zou, Yingrui Li, Xun Xu, Yong Zhang, Huanming Yang, Jian Wang, Jun Wang, Karl M. Kjer, Xin Zhou (2014): Phylogenomics resolves the timing and pattern of insect evolution. - Science 346 ( 6210): 763-767.

[more]

Links:

1KITE - Project @ ZFMK
Abstract
Reprint
Full text

Donath, A., Stadler, P.F. (2014): Molecular morphology: Higher order characters derivable from sequence information. In: Wägele, J.W. and Bartolomaeus, T. (eds.): Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New insights from analyses of molecules, morphology, and theory of data analyses.

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Peters, R.S.*, Meusemann, K.*, Petersen, M., Mayer, C., Wilbrandt, J., Ziesmann, T., Donath, A., et al. (2014): The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data. BMC Evolutionary Biology 14:52 http://www.biomedcentral.com/1471-2148/14/52 * equal contributors

[more]

Links:

Link - PDF

2013

BERNT M, BLEIDORN C, BRABAND A, DAMBACH J, DONATH A, FRITSCH G, GOLOMBEK A, HADRYS H, JÜHLING F, MEUSEMANN K, MITTENDORF M, MISOF B, PERSEKE M, PODSIADLOWSKI L, VON REUMONT B, SCHIERWATER B, SCHLEGEL M, SCHRÖDL M, SIMON S, STADLER PF, STÖGER I, STRUCK T (2013) A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol Phylogen Evol. Early online May 2013.

[more]

HANS-JÜRGEN OSIGUS, MICHAEL EITEL, MATTHIAS BERNT, ALEXANDER DONATH, BERND SCHIERWATER (2013) Mitogenomics at the base of Metazoa. Molecular Phylogenetics and Evolution, 69:339–351.

[more]

Meusemann, K., Peters, R.S., Petersen, M., Donath, A., Niehuis, O., Mayer, C., Aspöck, U. et al. (2013): Phylogeny of the holometabolous insect orders – new insights from transcriptomes and morphology. BioSyst.EU 2013 Global systematics! 18-22 February 2013 Abstract volume: 139-140.

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Niehuis, O., Sann, M., Mayer, C., Meusemann, K., Donath, A., Peters, R.S., Bleidorn, C., Ohl, M. (2013): Potential and limits of the 1KITE transcript data for facilitating the application of DNA enrichment protocols in insect phylogenetics. Abstract Volume 6th Dresden Meeting on Insect Phylogeny.

[more]

2012

BERNT, M., DONATH, A., JÜHLING, F., EXTERNBRINK, F., FLORENTZ, C., FRITZSCH, G., PÜTZ, J., MIDDENDORF, M., STADLER, P.F. (2012) MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol. Phylogenet. Evol.,

[more]

DONATH, A., MEUSEMANN, K. et al. (2012) Bioinformatic Challenges in the 1KITEProject. Annual Meeting of the Society for Molecular Biology and Evolution, SMBE (poster, co-author). 23.-26-06.2012

[more]

Pages

Work

since 05/2011
Research associate at the ZMB, ZFMK, Bonn, Germany.

11/2007 - 04/2011
Research Assistant at the Professur für Bioinformatik, Universität Leipzig, Germany.

09/2006 - 12/2006
Student apprentice at the TBI, University of Vienna, Austria.

10/2005 - 09/2006
Student assistant (SHK) at the Professur für Bioinformatik, Universität Leipzig, Germany.

05/2005 - 12/2005
Student assistant (SHK) at the Institut für Informatik, Universität Leipzig, Germany.

Studies

11/2007 - 05/2011
PhD studies at the Professur für Bioinformatik, Universität Leipzig, Germany. Thesis Title: "Molecular Morphology - Phylogenetically Informative Characters Derived from Sequence Data."

04/2007 - 10/2007
Diploma student at the Professur für Bioinformatik, Universität Leipzig, Germany. Thesis Title: "Tracing the TIRs - Expanding the repertoire of known TIR domain containing proteins."

09/2002 - 10/2007
Diploma studies in Computer Science (specialization in Bioinformatics), Universität Leipzig, Germany.

Grants

10/2006 - 12/2006
EU COST (European Cooperation in Science and Technology) action D27 STSM (Short Term Scientific Mission).

Consulting activities

since 06/2012
Member of the ecSeq Bioinformatics Scientific Advisory Board.

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Dr. Alexander Donath

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Research interests

Further information

2022

2017

2014

2012

2009

External projects

Pages

2018

2017

2016

2015

2014

2013

2012

Pages

Work

Studies

Grants

Consulting activities

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